Nice! It was perhaps a little harsh to front-load all that negativity--not that it all didn't ring true--but you pulled it out at the end: "We wouldn't be here if we didn't think the game was awesome." Came off rather triumphant, really.
I liked the game session, although I must admit my attention did wander a bit in the middle. Maybe it's too much like a "giant wall of text" to do a whole session all at once. Not sure how to fix that, though. Maybe try the old Batman routine? Break dramatically somewhere in the middle, do an intermission, then a "When we last left our Investigators…" finish?
You covered the question pretty thoroughly. I always throw down Clues anywhere (except open Gates, of course), because of a few cards that could get to them. (You hit on Yibb and Vision Quest, but there's also the Student Newspaper.)
As far as dilution: I think it really comes down to this. Either you avoid it entirely and only play with minimal expansions at once (like I do), or you play with as much as you want and always include Miskatonic Horror. Pros: The former only has to deal with one or two mechanics at once, usually focusing the theme on the expansions; the latter has true chaos in that you can never predict what craziness will happen next. Cons: Technically, the former is going to neglect a portion of your collection every game, but the latter puts theme, and often mechanics, in a blender on frappe, which could result in a sludgy coffee.